The complete chloroplast genome of Camellia flava (Pitard) Sealy, a golden camellia of Vietnam

Abstract Camellia flava (Pit.) Sealy 1949 is a rare and precious species with golden flowers, which hold important ornamental and breeding values. In this study, the complete chloroplast genome of C. flava is reported for the first time. The chloroplast genome exhibits a typical quadripartite structure with a total length of 156,670 bp and a GC content of 37.32%, including a large single-copy region (86,250 bp), a small single-copy region (18,292 bp), and a pair of inverted repeat regions (26,064 bp). A total of 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes were annotated. The phylogenetic analysis revealed a close relationship between C. flava and C. tamdaoensis. The chloroplast genome sequence of C. flava serves as a valuable resource for further breeding research and genetic phylogenetic studies.


Introduction
Camellia flava (Pit.)Sealy 1949, belonging to the genus Camellia L., is one species of golden camellias.It was first described by C.J. Pitard as Thea flava Pit. in 1910, then renamed by J.R. Sealy when the genus Thea was included in Camellia (Sealy 1958).This species is merely distributed in Vietnam, and usually grows in mixed forests of limestone mountains at altitudes of 250-600 meters.It holds significant horticultural and ornamental value because of its bright golden yellow flowers (Figure 1).Golden camellias often possess tea polyphenols and tea polysaccharides, which have high edible and medicinal values (He et al. 2018).However, due to the narrow distribution and small population of C. flava, there has been little research on it and the chloroplast genome has remained unknown.In this study, the complete chloroplast genome of C. flava was assembled and annotated based on Illumina double-end sequencing data, which would be beneficial for further breeding and utilization of this species.

Materials and methods
Young leaves were collected from cultivated species from the nursery of Yulin Normal University.(N 22.67, E 110.19), and the voucher specimens were preserved in the Laboratory of Plant Specimen of Fujian University of Science and Technology (voucher number: ST202304011, Contact: Guochang Ding, e-mail: yunxtang0319@163.com).We used an improved CTAB (Doyle and Doyle 1987) method to extract the total DNA of the sample.After that, the extracted total DNA was sent to BGI Technology Service Co., Ltd.(Wuhan, China) to construct a library, and the genome was sequenced using the Illumina HiSeq 4000 sequencing platform with a paired-end read length of 150 bp.The number of reads generated from sequencing was 32,021,479, and 438,786 reads were used to assemble the plastid genome.The chloroplast genome sequence was assembled using GetOrganelle v.3.11.0 (Jin et al. 2020).The parameters applied to the plastome assembly were -w 95 -R 20 -k 21, 35, 45, 55, 65, 75 -F embplant_pt.The assembled chloroplast genome was annotated using PGA (Qu et al. 2019), and the start codon and stop codon were manually adjusted using Geneious Prime (Kearse et al. 2012).CPGview (http://www.1kmpg.cn/cpgview) (Liu et al. 2023) was employed to generate genome maps of cis-spliced and trans-spliced genes.The assembled chloroplast genome and its detailed annotations were submitted to GeneBank with the accession number OR605723.

Discussion and conclusion
In this study, the chloroplast genome of Camellia flava was successfully sequenced and assembled.Like most angiosperms, the complete chloroplast genome of C. flava exhibits a typical quadripartite structure, including a large single-copy region (LSC), a small single-copy region (SSC), and two inverted repeat regions (IRs).Through research and analysis, it was found that the structure and gene content of the C. flava genome were similar to other published sect.Chrysantha genomes (Ding et al. 2022), which indicated that the C. flava chloroplast genome maintained relative conservation in the evolutionary process.This conservatism provides a solid basis for further comparative genome analysis and functional studies.In the phylogenetic analysis, the close relationship between C. flava and Camellia tamdaoensis was revealed.This finding was highly supported, suggesting that the two species may have a relatively close common ancestor and have maintained many common traits throughout evolution.
The genetic resources generated in this study are of great significance for the biological research, conservation, and breeding of C. flava.Genomic data can identify genes associated with important traits, assist breeders in selecting good individuals, and help track the genetic diversity and evolutionary history of populations, providing a scientific basis for conservation.The results of this study also provide valuable molecular resources for the phylogenetic and evolutionary study of C. flava and its relatives.In the future, with the accumulation of more data, more extensive genomic analysis can be carried out to further elucidate the evolutionary mechanism and functional characteristics.

Figure 2 .
Figure 2. The chloroplast genome map of Camellia flava.The species name is shown in the top left corner.The map contains six tracks.From the center outward, the first track shows the dispersed repeats.The dispersed repeats consist of direct (D) and Palindromic (P) repeats, connected with red and green arcs.The second track shows the long tandem repeats as short blue bars.The third track shows the short tandem repeats or microsatellite sequences as short bars with different colors.The colors, the type of repeat they represent, and the description of the repeat types are as follows.Black: c (complex repeat); green: p1 (repeat unit size ¼ 1); yellow: p2 (repeat unit size ¼ 2); purple: p3 (repeat unit size ¼ 3); blue: p4 (repeat unit size ¼ 4); orange: p5 (repeat unit size ¼ 5); red: p6 (repeat unit size ¼ 6).The small single-copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions are shown on the fourth track.The GC content along the genome is plotted on the fifth track.The genes are shown on the sixth track.Genes are color-coded by their functional classification.The transcription directions for the inner and outer genes are clockwise and anticlockwise, respectively.The functional classification of the genes is shown in the bottom left corner.